An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes

Research output: Contribution to journalJournal articleResearchpeer-review

Dorte B Bekker-Jensen, Christian D Kelstrup, Tanveer S Batth, Sara C Larsen, Christa Haldrup, Jesper B Bramsen, Karina D Sørensen, Søren Høyer, Torben F Ørntoft, Claus L Andersen, Michael L Nielsen, Jesper V Olsen

This study investigates the challenge of comprehensively cataloging the complete human proteome from a single-cell type using mass spectrometry (MS)-based shotgun proteomics. We modify a classical two-dimensional high-resolution reversed-phase peptide fractionation scheme and optimize a protocol that provides sufficient peak capacity to saturate the sequencing speed of modern MS instruments. This strategy enables the deepest proteome of a human single-cell type to date, with the HeLa proteome sequenced to a depth of ∼584,000 unique peptide sequences and ∼14,200 protein isoforms (∼12,200 protein-coding genes). This depth is comparable with next-generation RNA sequencing and enables the identification of post-translational modifications, including ∼7,000 N-acetylation sites and ∼10,000 phosphorylation sites, without the need for enrichment. We further demonstrate the general applicability and clinical potential of this proteomics strategy by comprehensively quantifying global proteome expression in several different human cancer cell lines and patient tissue samples.

Original languageEnglish
JournalCell Systems
Volume4
Issue number6
Pages (from-to)587-599, e1-e4
Number of pages18
ISSN2405-4712
DOIs
Publication statusPublished - 2017

    Research areas

  • Journal Article

Number of downloads are based on statistics from Google Scholar and www.ku.dk


No data available

ID: 184291218